Could we unintetnionally select for faster and more evasive fruit flies in the populations in our homes because we are always swatting at them. I hear they have a lot of genetic variation, and they lay eggs frequently.

I remember them being a pain to swat last summer. it was so difficult that we made a trap instead. Now, spring is back and the new wave is unimpressive. I could squash a few every few seconds when they were concentrated on the cieling above the kitchen light. I can put my thumb on them, and they don't even flinch. I spent more time whiping up the fly guts.

By the way, if there is a way to keep them out without killing them, I would appreciate your informativeness.

It definitely could, although it depends on how strong the selection is. I assume most of the fruit fly population reproduces in the wild, so the strongest selection factors are probably keeping them optimized for that environment. They might also already be at a maximum for what can be achieved with their particular body plan - since the selection we're applying isn't likely to differ too much from what they've encountered from predators in their evolutionary history.

I'm not sure how I would keep them out though, other than disposing of your organic waste (fruits, etc) as quickly as possible.